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2012 May 24
4
Manually modifying an hclust dendrogram to remove singletons
Dear R-Help,
I have a clustering problem with hclust that I hope someone can help
me with. Consider the classic hclust example:
hc <- hclust(dist(USArrests), "ave")
plot(hc)
I would like to cut the tree up in such a way so as to avoid small
clusters, so that we get a minimum number of items in each cluster,
and therefore avoid singletons. e.g. in this example, you can see
2004 Jul 21
2
Cutting heatmap dendrogram
...# genes
genes.distance <- as.dist(1-cor(set2));
genes.clusters <- hclust(genes.distance);
genes.dendrogr <- as.dendrogram(genes.clusters);
# samples
samples.distance <- as.dist(1-cor(set1));
samples.clusters <- hclust(samples.distance1);
samples.dendrogr <- as.dendrogram(samples.clusters1);
# cut the trees
samples.members <- cutree(samples.clusters, k=4);
genes.members <- cutree(genes.clusters, k=25);
# heatmap colouring
my.colors <- function(n = 20, low.col = 0.35, high.col=1, saturation = 0.85)
{
if (n < 2) stop("n must be greater than 2")
n1 <...